Methods and compositions for detecting BK virus
The invention provides methods and compositions for rapid, sensitive, and highly specific nucleic acid-based (e.g., DNA based) detection of a BK virus in a sample. In general, the methods involve detecting a target nucleic acid having a target sequence of a conserved region of BK viral genomes. The invention also features compositions, including primers, probes, and kits, for use in the methods of the invention.
1. A method of detecting the presence of BK virus (BKV) nucleic acid in a sample, the method comprising contacting said sample with one or more oligonucleotides designed to hybridize to SEQ ID NO: 57 or a complement thereof but not to JC virus nucleic acid under conditions which discriminate between BKV and JCV nucleic acid and detecting if the hybridization of said one or more oligonucleotides to SEQ ID NO: 57 or a complement thereof has occurred, wherein said hybridization detects the presence of BKV nucleic acid.
2. The method of claim 1 , wherein said step of detecting if hybridization has occurred comprises nucleic acid-based amplification.
3. The method of claim 2 , wherein said amplification generates a product about 30 nucleotides or less in length.
4. The method of claim 1 , further comprising detecting the presence of a second BKV nucleic acid in the sample, wherein said detecting a second BKV nucleic acid is achieved by contacting said sample with one or more oligonucleotides designed to hybridize to SEQ ID NO: 4 or a complement thereof but not to JC virus nucleic acid under conditions which discriminate between BKV and JCV nucleic acid and detecting if the hybridization of said one or more oligonucleotides to SEQ ID NO: 4 or a complement thereof has occurred, wherein said hybridization detects the presence of BKV nucleic acid.
5. The method of claim 2 , wherein said nucleic acid amplification is achieved by amplifying a portion of SEQ ID NO: 57 using primer pairs of SEQ ID NO: 12 and SEQ ID NO: 13 or a complement thereof.
6. The method of claim 1 , wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 57 or a complement thereof is a degenerate oligonucleotide.
7. The method of claim 1 , wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 57 or a complement thereof comprises a detectable label.
8. The method of claim 7 , wherein said detectable label is a fluorophore.
9. The method of claim 8 , wherein at least one or more of said oligonucleotides designed to hybridize to SEQ ID NO: 57 or a complement thereof comprises a quencher molecule.
10. The method of claim 9 , wherein the fluorophore and quencher molecule are attached to same oligonucleotide.
11. The method of claim 1 , wherein said step of detecting if hybridization has occurred comprises nucleic acid sequencing.
12. The method of claim 4 , wherein said detecting a second BKV nucleic acid is achieved by amplifying a portion of SEQ ID NO: 4 or complement thereof.
13. The method of claim 4 , wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 4 or a complement thereof is a degenerate oligonucleotide.
14. The method of claim 4 , wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 4 or a complement thereof comprises a detectable label.
15. The method of claim 14 , wherein said detectable label is a fluorophore.
16. The method of claim 15 , wherein at least one or more of said oligonucleotides designed to hybridize to SEQ ID NO: 4 or a complement thereof comprises a quencher molecule.
17. The method of claim 16 , wherein the fluorophore and quencher molecule are attached to same oligonucleotide.
18. The method of claim 4 , wherein said step of detecting if hybridization has occurred comprises nucleic acid sequencing.